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Jason Sahl jasonsahl

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  • Northern Arizona University
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@jasonsahl
jasonsahl / transpose_matrix.py
Created March 29, 2021 16:19
transpose a BSR matrix
#!/usr/bin/env python
import sys
from sys import argv
try:
out_matrix = open("transposed_matrix.matrix", "w")
reduced = []
with open(argv[1]) as my_file:
for line in my_file:
@jasonsahl
jasonsahl / mashPy.py
Last active February 17, 2022 15:57
Create a distance dendrogram from MASH distances
#!/usr/bin/env python
#A python implementation of building clusters from MASH distances
import optparse
import sys
from optparse import OptionParser
try:
from scipy.cluster.hierarchy import weighted
import scipy.spatial.distance as ssd
@jasonsahl
jasonsahl / parse_kmer_frequencies.py
Last active March 5, 2020 18:13
Parse Kmer frequencies from a Kmer matrix
#!/usr/bin/env python
"""parse frequencies from a Kmer matrix"""
from __future__ import division
import sys
import os
import optparse
from optparse import OptionParser
from collections import deque
@jasonsahl
jasonsahl / mlst_blast_assemblies.py
Last active November 1, 2018 18:02
Uses BLAST to perform MLST typing on genome assemblies
#!/usr/bin/env python
"""calculates MLST types from assemblies using BLAST.
If the gene is truncated, it will report a "T" and if
the gene has no blast hit, it will report a "X".
Your reference allele names must all end in "fasta"
and must contain a "_" between gene name and number.
The only external dependency is blast+ - tested version
is 2.2.31"""
@jasonsahl
jasonsahl / kallisto_wrapper.py
Created December 1, 2017 17:48
Kallisto read count wrapper
#!/usr/bin/env python
"""Read counts across a set of reference sequences.
Requires Python 2.7 to run"""
from __future__ import division
from __future__ import print_function
from optparse import OptionParser
import sys
import os
@jasonsahl
jasonsahl / 184_sra_ids.txt
Created October 23, 2017 16:52
ERR319438
ERR360775
ERR360792
ERR360848
ERR360746
ERR360782
ERR360788
ERR360789
ERR360783
ERR360770
@jasonsahl
jasonsahl / transform_kallisto_bacseq.py
Created July 17, 2017 19:37
Transfrom content of Kallisto matrix, used for in silico ribotyping of C. difficile in this case
#!/usr/bin/env python
"""Transform ribotype data. Input matrix
is a transposed output from bac_seq"""
from __future__ import print_function
from __future__ import division
import sys
import os
import optparse
@jasonsahl
jasonsahl / sum_seq_length.py
Created August 11, 2016 17:17
Calculates all bases in a multi-FASTA file
#!/usr/bin/python
#parses sequence lengths from a file and prints them to the screen
#usage python seqlength.py infasta
from __future__ import print_function
from sys import argv
import sys
try:
from Bio import SeqIO
except:
print("script requires BioPython to run..exiting")
@jasonsahl
jasonsahl / burk_clade_markers
Created September 2, 2015 19:41
This file has been truncated, but you can view the full file.
>Burkholderia_ambifaria_2
ATGCTCATGCGGCGGCTTGAGGTGACGTTCCCTTCTGACGGGGACGATTGTGCAGCTTGGCTATACCTTCCGGACACCAGCAGGCCGGCACCGGTGATCGTGATGGCACATGGTCTGGGCGGCACGCGTGAAATGCGACTGGATGCGTTTGCTCACAGATTCTGCGAGGCTGGATTTGCCTGTCTGGTGTTTGATTATCGGCACTTCGGCAGCAGTGGCGGCGAGCCGCGGCAGTTGCTCGATGTAGGCAAGCAGCTACAAGACTGGAGGGCCGCGATAGCATTTGCTCGAACACGAACCGACGTAGACGCAGAGAGATTGATTGTCTGGGGATCGTCGTTTGGGGGAGGGCATGCGCTGACCATCGCGGCCGACAACGCTCACGTGTCCGCGGTCATTGCCCAGTGTCCGTTCACGGATGGGCTGGCTTCCGTTTGCGCTTTACCATTAGGATCGCTAATCAAGGTAACTGCCAGAGCGATCCGCGATCAATTCCGCGCATGGTTGGGAGGGCACCCGGTGACCATCCCGATAGCCGGGAAGCCAGGGGGGGTTGCATTAATGGTGGCTCCTGATGCCGAGCCCGGCTACATGAAGTTGGTGCCGAACGATATGTCAGCCGTCTTTCGTAACTACGTGGCCGCCCGGTTCGCTCTTCAAATTATTCGCTATTTTCCCGGTCGCAAGACTTCACGGATCGCCTGCCCGGTGCTGTTCTGTGTTTGTGATCCTGATACCGTCGCGCCGACGCGTACTACGTTGCGTCACGCAAAACGTGCACCCAAAGGATTGGTGAATATATATCCGTTCGGACATTTCGATATTTATGTCGGTTATGCGTTTGAGCGGGCAGTCAGCGATCAAATCACCTTCCTTCAAAGATTCATTGATTAA
>Burkholderia_ambifaria_3
ATGAAATTCGACAACGTCCTGCAGACTATTGGCAATACCCCGATCATCCGCATGAATCGCCTGTTTGGCGCAGACGC
@jasonsahl
jasonsahl / HD_SNPs.txt
Created June 8, 2015 17:47
Chromosome start coord end coord #Parsimony-informative SNPs #Homoplasious SNPs Homoplasy density ratio
NC_011595 1 1001 3 3 1
NC_011595 1001 2001 2 2 1
NC_011595 2001 3001 5 5 1
NC_011595 3001 4001 2 1 0.5
NC_011595 4001 5001 0 0 0
NC_011595 5001 6001 0 0 0
NC_011595 6001 7001 0 0 0
NC_011595 7001 8001 0 0 0
NC_011595 8001 9001 1 1 1